
PFRMAT AL                                                                        
TARGET T0087                                                                     
REMARK =========================================================================
AUTHOR 6923-1755-6564                                                           
REMARK Ralf Zimmer, GMD-SCAI,                                                   
REMARK Theo Mevissen, GMD-SCAI,                                                 
REMARK Ingolf Sommer, GMD-SCAI,                                                 
REMARK Thomas Lengauer, GMD-SCAI,                                               
REMARK German National Research Center for Information Technology               
REMARK Institute for Algorithms and Scientific Computing                        
REMARK =========================================================================
METHOD A reduced candidate list is produced via ToPLign [1]                     
METHOD sequence/profile alignments, 123D [2] and RDP [3].                       
METHOD The top scoring candidates from this list and the                        
METHOD corresponding refined alignments have been produced                      
METHOD with RDP [3] using newly derived modifications of                        
METHOD contact capacity [2] and pair interaction potentials.                    
METHOD References:                                                              
METHOD [1] Heinz Mevissen and Ralf Thiele and Ralf Zimmer and Thomas Lengauer:  
METHOD     "Analysis of Protein Alignments -- The software environment ToPLign",
METHOD     GMD, 1994-98.                                                        
METHOD [2] Nick Alexandrov and Ruth Nussinov and Ralf Zimmer:                   
METHOD     "Fast Protein Fold Recognition via Sequence to Structure Alignment   
METHOD     and Contact Capacity Potentials",                                    
METHOD     Pacific Symposium on Biocomputing'96, World Scientific Publ. Co.,    
METHOD     1996, 53--72.                                                        
METHOD [3] Ralf Thiele and Ralf Zimmer and Thomas Lengauer:                     
METHOD     "Recursive Dynamic Programming for Adaptive Sequence                 
METHOD     and Structure Alignment",                                            
METHOD     ISMB'95, C. Rawlings et al. (Eds.), AAAI Press, 384--392.            
METHOD [4] Ralf Thiele and Ralf Zimmer and Thomas Lengauer:                     
METHOD     "Protein Threading by Recursive Dynamic Programming",                
METHOD     JMB,757-779,290,1999                                                 
METHOD [5] Ralf Zimmer and Marko Woehler and Ralf Thiele:                       
METHOD     "New Scoring Schemes for Protein Fold Recognition                    
METHOD     based on Voronoi Contacts",                                          
METHOD     Bioinformatics, 14, 3, 295--308, 1998.                               
METHOD [6] Alexander Zien and Ralf Zimmer and Thomas Lengauer:                  
METHOD     "A simple iterative approach to parameter optimization",             
METHOD     JCB, 2000, in press.                                                 
REMARK =========================================================================
MODEL  1                                                                         
PARENT 2HLP_A                                                                    
S   2    T    22                                                                 
K   3    K    23                                                                 
I   4    V    24                                                                 
L   5    S    25                                                                 
V   6    V    26                                                                 
F   7    V    27                                                                 
G   8    G    28                                                                 
H   9    A    29A                                                                
S  14    A    29B                                                                
D  15    G    30                                                                 
A  16    T    31                                                                 
I  17    V    32                                                                 
G  18    G    33                                                                 
S  19    A    34                                                                 
S  20    A    35                                                                 
M  21    A    36                                                                 
A  22    G    37                                                                 
Y  23    Y    38                                                                 
A  24    N    39                                                                 
Y  25    I    40                                                                 
L  26    A    41                                                                 
K  27    L    42                                                                 
R  28    R    43                                                                 
G  31    D    44                                                                 
V  32    I    45                                                                 
D  33    A    46                                                                 
A  34    D    47                                                                 
Q  35    E    48                                                                 
A  36    V    49                                                                 
V  37    V    50                                                                 
A  38    F    51                                                                 
L  39    V    52                                                                 
G  40    D    53                                                                 
N  41    I    54A                                                                
P  42    P    54B                                                                
N  43    D    54C                                                                
E  44    K    55                                                                 
E  45    E    56                                                                 
T  46    D    57                                                                 
A  47    D    58                                                                 
F  48    T    59                                                                 
V  49    V    60                                                                 
L  50    N    67                                                                 
D  51    H    68                                                                 
Y  52    G    69                                                                 
F  53    I    70                                                                 
G  54    A    71                                                                 
I  55    Y    72                                                                 
Q  56    D    73                                                                 
A  57    S    74                                                                 
P  58    N    75                                                                 
P  59    T    76                                                                 
V  60    R    77                                                                 
V  61    V    78                                                                 
K  62    R    79                                                                 
S  63    Q    80                                                                 
A  64    G    81                                                                 
Q  65    G    84                                                                 
A  66    T    88                                                                 
E  67    A    89                                                                 
G  68    G    90                                                                 
A  69    S    91                                                                 
K  70    D    92                                                                 
Q  71    V    93                                                                 
V  72    V    94                                                                 
I  73    V    95                                                                 
L  74    I    96                                                                 
T  75    T    97                                                                 
D  76    A    98                                                                 
H  77    G    99                                                                 
N  78    I   100                                                                 
E  79    P   101                                                                 
F  80    R   102                                                                 
Q  81    Q   103                                                                 
Q  82    P   105                                                                 
S  83    G   106                                                                 
I  84    Q   107                                                                 
A  85    T   108                                                                 
D  86    R   109                                                                 
I  87    I   110                                                                 
R  88    D   111                                                                 
E  89    L   112                                                                 
V  90    A   113                                                                 
E  91    D   115                                                                 
V  92    N   116                                                                 
V  93    A   117                                                                 
E  94    P   118                                                                 
V  95    I   119                                                                 
V  96    M   120                                                                 
D  97    E   121                                                                 
H  98    D   122                                                                 
H  99    I   123                                                                 
V 101    Q   124                                                                 
A 102    S   125                                                                 
N 103    S   126                                                                 
F 104    L   127                                                                 
E 105    D   128                                                                 
T 106    E   129                                                                 
A 107    H   130                                                                 
N 108    N   131                                                                 
P 109    D   132A                                                                
L 110    D   132B                                                                
Y 111    Y   133                                                                 
M 112    I   134                                                                 
R 113    S   135                                                                 
L 114    L   136                                                                 
E 115    T   137                                                                 
P 116    T   138                                                                 
V 117    S   139                                                                 
G 118    N   140                                                                 
S 119    P   141                                                                 
A 120    V   142                                                                 
S 121    D   143                                                                 
S 122    L   144                                                                 
I 123    L   145                                                                 
V 124    N   146                                                                 
Y 125    R   147                                                                 
R 126    H   148                                                                 
L 127    L   149                                                                 
Y 128    Y   150                                                                 
K 129    E   151                                                                 
E 130    A   152                                                                 
N 131    G   153                                                                 
G 132    D   154                                                                 
V 133    R   155                                                                 
A 134    S   156                                                                 
I 135    R   157                                                                 
I 139    E   158                                                                 
A 140    Q   159                                                                 
G 141    V   160                                                                 
V 142    I   161                                                                 
M 143    G   162                                                                 
L 144    F   163                                                                 
S 145    G   164                                                                 
V 166    G   165                                                                 
A 167    R   166                                                                 
E 168    L   167                                                                 
D 169    D   168                                                                 
L 170    S   169                                                                 
A 171    A   170                                                                 
K 172    R   171                                                                 
I 173    F   172                                                                 
A 174    R   173                                                                 
G 175    Y   174                                                                 
V 176    V   175                                                                 
D 177    L   176                                                                 
L 178    S   177                                                                 
Q 179    E   178                                                                 
E 180    E   179                                                                 
Y 181    F   180                                                                 
G 182    D   181                                                                 
L 183    A   182                                                                 
A 184    P   183                                                                 
M 185    V   184                                                                 
L 186    Q   185                                                                 
K 187    N   186                                                                 
A 188    V   187                                                                 
G 189    E   188                                                                 
T 190    G   189                                                                 
N 191    T   190                                                                 
L 192    I   191                                                                 
A 193    L   192                                                                 
S 194    G   193                                                                 
K 195    E   194                                                                 
T 196    H   195                                                                 
A 197    G   196                                                                 
A 198    D   197                                                                 
Q 199    A   198                                                                 
L 200    Q   199                                                                 
V 201    V   200                                                                 
D 202    P   201                                                                 
I 203    V   202                                                                 
D 204    F   203                                                                 
A 205    S   204                                                                 
K 206    K   205                                                                 
F 208    V   206                                                                 
E 209    R   207                                                                 
L 210    V   208                                                                 
N 211    D   209                                                                 
G 212    G   210A                                                                
S 213    T   210B                                                                
Q 214    D   211                                                                 
V 215    P   212                                                                 
R 216    E   219                                                                 
V 217    F   220                                                                 
A 218    S   221                                                                 
Q 219    G   222                                                                 
V 223    D   223                                                                 
D 224    E   224                                                                 
I 225    K   225                                                                 
N 226    E   226                                                                 
E 227    Q   227                                                                 
V 228    L   228                                                                 
L 229    L   229                                                                 
E 230    G   230                                                                 
R 231    D   231                                                                 
Q 232    L   232                                                                 
N 233    Q   233                                                                 
E 234    E   234                                                                 
I 235    S   235                                                                 
E 236    A   236                                                                 
E 237    M   237                                                                 
A 238    D   238                                                                 
I 239    V   239                                                                 
K 240    I   240                                                                 
A 241    E   241                                                                 
S 242    R   242                                                                 
Q 243    K   243                                                                 
A 244    G   244                                                                 
A 245    A   245                                                                 
N 246    T   246                                                                 
G 247    E   247                                                                 
Y 248    W   248                                                                 
S 249    G   249                                                                 
D 250    P   250                                                                 
F 251    V   254                                                                 
V 252    A   255                                                                 
L 253    H   256                                                                 
M 254    M   257                                                                 
I 255    V   258                                                                 
T 256    E   259                                                                 
D 257    A   260                                                                 
I 258    I   261                                                                 
L 259    L   262                                                                 
N 260    H   263                                                                 
S 261    D   264                                                                 
N 262    T   265                                                                 
S 263    G   266                                                                 
E 264    R   267                                                                 
I 265    V   268                                                                 
L 266    L   269                                                                 
A 267    P   270                                                                 
L 268    A   271                                                                 
G 269    S   272                                                                 
N 270    V   273                                                                 
K 274    K   274                                                                 
V 275    L   275                                                                 
E 276    E   276                                                                 
A 277    G   277                                                                 
A 278    E   278                                                                 
F 279    F   279                                                                 
N 280    E   304                                                                 
F 281    W   305                                                                 
T 282    D   306                                                                 
L 283    L   307                                                                 
K 284    D   308                                                                 
N 285    D   309                                                                 
N 286    E   311                                                                 
H 287    Q   312                                                                 
A 288    D   313                                                                 
F 289    L   314                                                                 
L 290    M   315                                                                 
A 291    A   316                                                                 
G 292    D   317                                                                 
A 293    A   318                                                                 
V 301    A   319                                                                 
P 302    E   320                                                                 
Q 303    K   321                                                                 
L 304    L   322                                                                 
T 305    S   323                                                                 
E 306    D   324                                                                 
S 307    Q   325                                                                 
F 308    Y   326                                                                 
N 309    D   327                                                                 
G 310    S   330                                                                 
TER                                                                              
END                                                                              



